Showing : affycoretools • reset
0
votes
3
replies
228
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 5 months ago by 57k • written 6 months ago by • 0
0
votes
2
replies
165
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
7 months ago luca.piacentini • 0
4
votes
5
replies
213
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 15 months ago by 57k • written 15 months ago by ▴ 780
3
votes
5
replies
245
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 18 months ago by 57k • written 18 months ago by ▴ 40
1
vote
2
replies
306
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 23 months ago by 57k • written 23 months ago by ★ 3.0k
1
vote
5
replies
325
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 780
0
votes
3
replies
792
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 3.0 years ago by 57k • written 3.0 years ago by • 0
2
votes
4
replies
519
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 3.3 years ago by 57k • written 3.3 years ago by ▴ 10
1
vote
3
replies
552
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 3.4 years ago by 57k • written 3.4 years ago by ▴ 60
2
votes
4
replies
1.2k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 3.8 years ago by 57k • written 3.8 years ago by ▴ 30
2
votes
3
replies
874
views
Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
pd.hta.2.0 hta2.0 affycoretools
updated 3.8 years ago by 57k • written 3.8 years ago by ▴ 20
5
votes
4
replies
1.8k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 4.2 years ago by 57k • written 4.2 years ago by ▴ 780
9
votes
6
replies
2.7k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 4.4 years ago by 57k • written 4.4 years ago by ▴ 780
0
votes
3
replies
845
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 4.4 years ago by 57k • written 4.4 years ago by ★ 2.0k
3
votes
5
replies
808
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 6.2 years ago by 57k • written 6.2 years ago by ★ 2.0k
0
votes
4
replies
1.9k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 7.1 years ago by 33k • written 7.1 years ago by ▴ 50
0
votes
3
replies
1.3k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 8.2 years ago by 57k • written 8.2 years ago by ★ 2.0k
0
votes
0
replies
790
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
8.2 years ago Fiona ▴ 70
0
votes
7
replies
879
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 10.1 years ago by 57k • written 10.1 years ago by ▴ 350
0
votes
1
reply
641
views
why kOverA function has 6
affycoretools affycoretools
updated 10.1 years ago by ▴ 20 • written 10.1 years ago by ★ 2.0k
0
votes
0
replies
674
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
10.3 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
618
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 10.3 years ago by 57k • written 10.3 years ago by ★ 1.5k
0
votes
3
replies
964
views
Help in installing affycoretools
affycoretools affycoretools
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 350
0
votes
0
replies
703
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
12.0 years ago James W. MacDonald 57k
0
votes
4
replies
2.8k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
12.6 years ago Celine Carret ▴ 220
0
votes
0
replies
640
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
12.7 years ago James W. MacDonald 57k
0
votes
2
replies
1.1k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 12.7 years ago by 57k • written 12.7 years ago by ▴ 80
0
votes
0
replies
664
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
12.7 years ago rgentleman ★ 5.5k
0
votes
3
replies
860
views
affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 13.0 years ago by 57k • written 13.0 years ago by ▴ 160
0
votes
1
reply
649
views
affycoretools question
GO limma affycoretools GO limma affycoretools
updated 13.0 years ago by 57k • written 13.0 years ago by ▴ 160
0
votes
10
replies
798
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 13.8 years ago by ★ 2.2k • written 13.8 years ago by ★ 7.4k
0
votes
3
replies
694
views
intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 14.2 years ago by 57k • written 14.2 years ago by ★ 2.2k
0
votes
3
replies
1.1k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 14.2 years ago by 57k • written 14.2 years ago by ★ 2.2k
0
votes
2
replies
794
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO Survival Biobase genefilter affy limma RBGL GOstats Category affyio affycoretools GO
14.4 years ago Mark W Kimpel ▴ 830
0
votes
1
reply
479
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 14.4 years ago by 57k • written 14.4 years ago by ▴ 830
0
votes
5
replies
831
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 14.6 years ago by ★ 7.4k • written 14.6 years ago by ▴ 890
0
votes
0
replies
585
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
14.6 years ago Kimpel, Mark W ▴ 890
0
votes
3
replies
2.7k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 14.6 years ago by 57k • written 14.6 years ago by ▴ 320
0
votes
0
replies
607
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
14.6 years ago James W. MacDonald 57k
0
votes
2
replies
733
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
15.0 years ago Kimpel, Mark W ▴ 890
0
votes
1
reply
435
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 15.2 years ago by 57k • written 15.2 years ago by ▴ 890
0
votes
6
replies
820
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 15.3 years ago by 57k • written 15.3 years ago by ▴ 20
0
votes
2
replies
627
views
justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
15.4 years ago Kimpel, Mark W ▴ 890
43 results • Page 1 of 1
Recent ...
Replies
Comment: Determining number of genes in each module based on color in WGCNA package by schum266 • 0
For anyone who might be interested. I was able to figure this out. It's very easy.... just set numericLabels = FALSE. (*sigh*) ``` net = …
Comment: Research fellow in immunology by ATpoint ▴ 640
Try starting a new R session and then load the package again. If that fails then manually install ellipsis version 0.3.2 or greater. By the…
Answer: Creating the correct model to account for paired-samples (patient-effect) help n by Gordon Smyth 43k
In the limma User's Guide, Section 9.4.1 *Paired Samples* covers paired designs. In the edgeR User's Guide, it is Section 3.4.1.
Comment: How to convert .CEL file to .VCF file? by jesus • 0
Thank you! I'd already seen it, but the problem is that I'm using Windows and I think that code is only for Linux. Thanks anyway!
Comment: DESeq2 codes by Ram ▴ 60
DESeq2 is a piece of software that can be used to find statistically significant differential expression in RNAseq datasets. See: https://b…
Votes
Comment: What is the correct use of removeBatchEffect's design parameter
Answer: DESeq2 for allele-specific expression with contrasts between conditions
C: DESeq2 question about use of DESeqDataSetFromTximport() from RSEM data
Comment: Data input for aracne2regulon function in viper package
Comment: DESeq2: NA's in mcols(object)$betaConv
Awards • All
Popular Question to Gordon Smyth 43k
Popular Question to tcalvo ▴ 40
Popular Question to Malcolm Cook ★ 1.5k
Popular Question to Keith Hughitt ▴ 140
Scholar to Aaron Lun ★ 26k
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